In recent years, square hollow section (SHS) joints with concrete-filled square hollow section (CFSHS) chords have increasingly been used in truss bridges where the fatigue life reliability is a critical issue. In this paper, a finite element analysis was performed to investigate the SCFs in SHS-CFSHS T-joints under in-plane bending in the brace, axial force in the chord and in-plane bending in the chord. The finite element models were developed and validated with experimental results. Then a parametric study was conducted with a reasonable range of three key non-dimensional parameters, i.e., β (width ratio between brace and chord), 2γ (width–to–wall thickness ratio of the chord) and τ (wall thickness ratio between brace and chord). Consequently, the stress concentration factor formulae for the fatigue design of SHS-CFSHS T-joints were proposed through multiple regression analysis. For in-plane bending in the brace, the maximum stress concentration factors were found at lines B and C for thick-walled chords (2γ = 25.0), while the stress concentration factors at all the lines need to be checked for thin-walled chords (2γ < 16.0). Under axial force in the chord and in-plane bending in the chord, only stress concentration factors at lines C and D needed to be considered. A comparison of stress concentration factors between SHS-SHS and SHS-CFSHS joints showed reductions of 10~26% and 14~31% in stress concentration factors in SHS-CFSHS joints under axial force in the brace and in-plane bending in the brace, respectively. In addition, it showed a general increase in stress concentration factors in SHS-CFSHS joints under axial force and in-plane bending in the chord. This reduction is attributed to the reduction in chord face deformation benefiting from the in-filled concrete. Meanwhile, the stress concentration factors caused by loads in the chord are much lower than those caused by loads in the brace. This work complements earlier studies on SHS-CFSHS T-joints under axial force.